RDKit Add Conformers

Creates a new table with multiple conformers per input molecule. Each conformer is a copy of the molecule with different coordinates assigned. Each conformer row is mapped back to the input table molecule with an identifier - usually the row id - taken from an input table column.

Options

Input

RDKit Mol column

The input column with RDKit Molecules.

Reference column (e.g. an ID)

The input column with reference data to be assigned to conformer rows.

Conformer Calculation

Number of conformers

Number of conformers to be generated.

Maximum number of tries to generate conformers

Maximum number of tries that the RDKit will use to generate conformers. 0 means that the RDKit code sets the value to 10 times the number of atoms.

Random seed

A random seed to initialize random number generator.

RMS threshold for keeping a conformer

The RMS threshold for keeping a conformer.

Output

Column name for molecules with conformers

The output column with the generated conformers.

Column name for copied reference data

The output column with reference data taken from the input table.

Advanced

Enforce the preservation of input chirality

Ensures that the chirality/bond stereochemistry specified in the input structures is reflected in the conformers.

Use experimental torsion angle terms

Use data from experimental crystal structures to refine some torsion angles. This uses the "ET" method described in https://doi.org/10.1021/acs.jcim.5b00654 and https://doi.org/10.1021/acs.jcim.0c00025 .

Experimental torsion angles version

Choose the version of the experimental torsion definitions to use. Possible values are 1 and 2.

Use experimental torsion angle terms for small rings

Use data from experimental crystal structures to refine some torsion angles in small rings. This uses the "srET" method described in https://doi.org/10.1021/acs.jcim.0c00025 .

Use experimental torsion angle terms for macrocycles

Use data from experimental crystal structures to refine some torsion angles in macrocycles. This uses the method described in https://doi.org/10.1021/acs.jcim.0c00025 .

Use 1-4 distance bound heuristics for macrocycles

Use empirical corrections to modify 1-4 distance bounds in macrocycles. T his uses the method described in https://doi.org/10.1021/acs.jcim.0c00025 .

Use basic knowledge terms

Apply "basic knowledge" constraints to planarize atoms which should be planar (e.g. aromatic atoms, conjugated atoms). This uses the "K" method described in https://doi.org/10.1021/acs.jcim.5b00654 .

Force amide bonds to be trans

Applies constraints to force amide, ester, and related bonds to have trans configurations.

Only use heavy atoms when calculating RMS values

When doing RMS pruning only heavy atoms will be used to calculate RMS.

Use molecular symmetry when pruning conformers

When doing RMS pruning molecular symmetry will be taken into account. Note that for reasons of computation efficiency, when this option is enabled only heavy atoms will be used in the RMS calculation.

Embed fragments separately

Embed each of the molecule's fragments individually. Each fragment will be centered at the origin (i.e. the fragments will overlap). When this option is disabled, the fragments will not overlap but attractive inter-fragment interactions (e.g. H-bonds) are not taken into account.

Use random coordinates as a starting point instead of distance geometry

Setting this flag will use random coordinates as a starting point instead of distance geometry.

Multiplier for the size of the box for random coordinates

Specifies a multiplier for the size of the box for random coordinates.

Perform a cleanup using UFF (Universal force field) after calculation

Set this flag to perform cleanup with UFF after the conformer's calculation. Just clear this flag to output unprocessed conformers in case you want to perform other processing on them before cleaning them up with a force field.

Views

This node has no views

Workflows

• (3D) Fragment library design workflow v1.1KNIME Hub
• 05_Working_In_3DKNIME Hub
• 3D Molecule Viewer ExampleKNIME Hub
• Basic 3D Alignment NGLKNIME Forum
• geometry optimizationKNIME Forum
• Show all 16 workflows

Links

• No links available

Developers